Neurodegenerative diseases are among the most expensive, disruptive, and least well treated of human maladies, arguably because they are not well understood. Array Tomography is a new method for tissue imaging with resolution in all three dimensions sufficient to resolve individual synapses and provide quantitative characterization of multiple (currently ~40) molecular constituents, throughout large samples. Array Tomography imaging data enable description of neural networks in the context of the three-dimensional tissue architecture. We believe such data will enable researchers to begin to comprehend the proper function of neural circuits and, importantly, to begin to understand how it is that the various neurodegenerative processes present and progress. Array Tomography is, however, complex and expensive, and has been used in relatively few studies following the first publication in 2007 (Micheva and Smith, 2007). Aratome is currently offering Array Tomography services to the research community. The present application proposes the development of a software application that automates the assembly of the multi- channel image volumes and provides tools to analyze those data. Assembling and analyzing data constitute the current bottleneck in producing and using high quality Array Tomography data. The package will be used internally and made available as a product to the research community.